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A balanced measure shows superior performance of pseudobulk methods over mixed models and pseudoreplication approaches in single-cell RNA-sequencing analysis

Alan Murphy, Nathan Skene

CUT&Tag recovers up to half of ENCODE ChIP-seq peaks

Di Hu, Leyla Abbasova, Brian Schilder, Alexi Nott, Nathan Skene, Sarah Marzi

Genetic variation at mouse and human ribosomal DNA influences associated epigenetic states

Francisco Rodriguez-Algarra, Robert AE Seaborne, Amy F Danson, Selin Yildizoglu, Harunori Yoshikawa, Pui Pik Law, Zakaryya Ahmad, Victoria A Maudsley, Ama Brew, Nadine Holmes, others

Multidimensional Dynamics of the Proteome in the Neurodegenerative and Aging Mammalian Brain

Byron Andrews, Alan Murphy, Michele Stofella, Sarah Maslen, Leonardo Almeida-Souza, J Mark Skehel, Nathan Skene, Frank Sobott, René AW Frank

Altered perivascular fibroblast activity precedes ALS disease onset

Anna Månberg, Nathan Skene, Folkert Sanders, Marta Trusohamn, Julia Remnestål, Anna Szczepinska, Inci Sevval Aksoylu, Peter Lönnerberg, Lwaki Ebarasi, Stefan Wouters, others

CHAS, a deconvolution tool, infers cell type-specific signatures in bulk brain histone acetylation studies of brain disorders

Kitty Murphy, Alexi Nott, Sarah Marzi

Chd8 regulates X chromosome inactivation in mouse through fine-tuning control of Xist expression

Andrea Cerase, Alexander N Young, Nerea Blanes Ruiz, Andreas Buness, Gabrielle M Sant, Mirjam Arnold, Monica Di Giacomo, Michela Ascolani, Manish Kumar, Andreas Hierholzer, others

Conditional GWAS analysis to identify disorder-specific SNPs for psychiatric disorders

Enda M Byrne, Zhihong Zhu, Ting Qi, Nathan Skene, Julien Bryois, Antonio F Pardinas, Eli Stahl, Jordan W Smoller, Marcella Rietschel, Michael J Owen, others

MungeSumstats: a Bioconductor package for the standardization and quality control of many GWAS summary statistics

Alan Murphy, Brian Schilder, Nathan Skene

ScFlow: A scalable and reproducible analysis pipeline for single-cell RNA sequencing data

Combiz Khozoie, Nurun Fancy, Mahdi M Marjaneh, Alan Murphy, Paul M Matthews, Nathan Skene